Source-separated human urine may be used as a source of fertilizers indirectly through processing with clinoptilolite. The suggested form of fertilizer is clinoptilolite loaded with plant nutrients from urine, where nitrogen and phosphorus will be released upon contact with water. Triggered by the need for handling high concentrations remaining in the liquid phase to be disposed of, this paper aims to present the option of improving the residual nutrient quality through stagewise processing with clinoptilolite, while investigating any improvement in nutrient removal. Two sets of experiments, stagewise operation under (i) constant loadings and (ii) variable loadings in each stage, are discussed. Stagewise operation has been observed to be successful for attaining reduced residual liquid phase concentrations as well as improvements in nitrogen recovery as compared to single-stage operation. Comparing constant and variable stagewise loadings, the final concentration is 10 times lower with variable loadings. The latter is comparable to a level found in only 1% of conventional domestic wastewater volume. Stagewise operation was beneficial from the standpoint of both additional nutrient recovery and for residuals control, with more pronounced benefits for attaining higher quality residual liquid phase concentrations to be disposed of.